dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Apr 29, 2011 at 09:52:25AM +0100, Garth N. Wells wrote:
>
>
> On 29/04/11 09:50, Anders Logg wrote:
> > On Fri, Apr 29, 2011 at 10:31:07AM +0200, Martin Sandve Alnæs wrote:
> >> On 29 April 2011 10:20, Anders Logg <logg@xxxxxxxxx> wrote:
> >>> On Fri, Apr 29, 2011 at 09:15:51AM +0100, Garth N. Wells wrote:
> >>>>
> >>>>
> >>>> On 29/04/11 08:58, Martin Sandve Alnæs wrote:
> >>>>> On 29 April 2011 09:35, Anders Logg <logg@xxxxxxxxx> wrote:
> >>>>>> On Thu, Apr 28, 2011 at 10:48:28PM +0100, Garth N. Wells wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>> On 28/04/11 22:17, Anders Logg wrote:
> >>>>>>>> On Thu, Apr 28, 2011 at 12:55:02PM +0200, Martin Sandve Alnæs wrote:
> >>>>>>>>> On 28 April 2011 11:45, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> On 27/04/11 20:50, Johan Hake wrote:
> >>>>>>>>>>> On Wednesday April 27 2011 12:45:46 Martin Sandve Alnæs wrote:
> >>>>>>>>>>>> On 27 April 2011 21:34, Anders Logg <logg@xxxxxxxxx> wrote:
> >>>>>>>>>>>>> On Wed, Apr 27, 2011 at 09:30:08PM +0200, Martin Sandve Alnæs wrote:
> >>>>>>>>>>>>>> 2011/4/27 Johan Hake <johan.hake@xxxxxxxxx>
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     On Wednesday April 27 2011 12:03:56 Martin Sandve Aln s wrote:
> >>>>>>>>>>>>>>     > On 27 April 2011 19:07, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >>>>>>>>>>>>>>     > > I'm starting here a new thread on how to deal with the recent
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> change in
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > > UFL that has broken a good number of DOLFIN demos. The previous
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> thread
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > > meandered and got side-tracked.
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > The framework in we need to operate is:
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > A. UFL will not allow forms to be modified post-construction.
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > B. It should be relatively easy to replace ufl.Coefficients in
> >>>>>>>>>>>>>>     > > a
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> form
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > > and return a new form.
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > C. The issue with replacing ufl.Coefficients is that we lose
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> DOLFIN
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     data
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > > (like the eval() functions) associated with the removed
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> coefficients.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > > I'll kick off with the obvious solution:
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > 1. Require that all DOLFIN Expressions are associated with a
> >>>>>>>>>>>>>>     > > ufl.FiniteElement.
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > Other solutions?
> >>>>>>>>>>>>>>     > >
> >>>>>>>>>>>>>>     > > Garth
> >>>>>>>>>>>>>>     >
> >>>>>>>>>>>>>>     > 2.  At the stage when ffc calls ufl.preprocess, or even in
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     ufl.preprocess,
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > let the preprocessed form contain ufl Coefficients with new
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> elements in
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > place of the dolfin.Expressions. This is similar to the
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> replacements done
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > for renumbering of Coefficients, and could either be done
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> simultaneously
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     or
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > as an additional step. The original Form and Expression objects
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> will be
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     > untouched, and the preprocessed form will be fine.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     +
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>     However, setting cell and degree is done during analysis and relies
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> on
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     form_data. The form is also preprocessed when the form_data is
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> extracted.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     This
> >>>>>>>>>>>>>>     means that for the preprocessed form to get correct signature, cell
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> and
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>>     degrees being set, we need to break up the logic.
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>>      1) extract form_data
> >>>>>>>>>>>>>>      2) set degree and cell
> >>>>>>>>>>>>>>      3) genererate preprocessed form
> >>>>>>>>>>>>>>
> >>>>>>>>>>>>>> Lets figure out the exact algorithm if we need it. It could perhaps be
> >>>>>>>>>>>>>> integrated better with preprocess. Or it might be better to extract
> >>>>>>>>>>>>>> just
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> the
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> information needed to determine degree and cell first, and pass the
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> element
> >>>>>>>>>>>>>
> >>>>>>>>>>>>>> replacements to preprocess.
> >>>>>>>>>>>>>
> >>>>>>>>>>>>> That's what I suggested in an earlier mail. Preprocess already gets
> >>>>>>>>>>>>> common_cell. We could also figure out common_degree before calling
> >>>>>>>>>>>>> preprocess but that requires getting the data stored in
> >>>>>>>>>>>>> form_data.sub_elements.
> >>>>>>>>>>>>
> >>>>>>>>>>>> Extracting all sub elements from a form before preprocessing should be easy
> >>>>>>>>>>>> and efficient.
> >>>>>>>>>>>>
> >>>>>>>>>>>> I assume it's still possible to construct an Expression with a specific
> >>>>>>>>>>>> FunctionSpace?
> >>>>>>>>>>>
> >>>>>>>>>>> Yes.
> >>>>>>>>>>>
> >>>>>>>>>>
> >>>>>>>>>> So it seems we've reached a solution that won't require any changes to
> >>>>>>>>>> DOLFIN, and only minimal changes to FFC. The story is:
> >>>>>>>>>>
> >>>>>>>>>> 1. UFL will permit elements without a cell and without a degree. The
> >>>>>>>>>> will leads an error for some operations, like grad and div.
> >>>>>>>>>>
> >>>>>>>>>> 2. Add a function to UFL to extract all sub-elements from a form.
> >>>>>>>>
> >>>>>>>> The functionality is already there since this is already extracted in
> >>>>>>>> the preprocess function.
> >>>>>>>>
> >>>>>>>
> >>>>>>> We need a function to do this before preprocess in order to pass the
> >>>>>>> cell and element types to the preprocess function.
> >>>>>>
> >>>>>> Yes, but as I just said, we already do that inside preprocess (by
> >>>>>> calling extract_sub_elements) so the functionality is already there to
> >>>>>> be used.
> >>>>>>
> >>>>>>>>>> 3. Add 'unspecified_elements=[]' (perhaps a dict?) to the argument list
> >>>>>>>>>> of ufl.algorithms.preprocess.
> >>>>>>>>
> >>>>>>>> Not sure if this is needed.
> >>>>>>>>
> >>>>>>>>>> 4. For coefficients with incomplete elements, preprocess will replace
> >>>>>>>>>> these with coefficients based on elements from the list
> >>>>>>>>>> 'unspecified_elements'. The new form will be the 'preprocessed form'.
> >>>>>>>>>>
> >>>>>>>>>> Is that it? Anything else?
> >>>>>>>>>>
> >>>>>>>>>> Garth
> >>>>>>>>>
> >>>>>>>>> I think that should be all.
> >>>>>>>>
> >>>>>>>> I think all we need to do (in FFC) is to
> >>>>>>>>
> >>>>>>>> 1. extract the minimal amount of data we need to decide the undecided
> >>>>>>>> degree and cell (essentially building the list of elements)
> >>>>>>>>
> >>>>>>>> 2. select the degree and cell (as we do today)
> >>>>>>>>
> >>>>>>>> 3. pass the degree and cell to compute_form_data (and thus to
> >>>>>>>> preprocess)
> >>>>>>>>
> >>>>>>>
> >>>>>>> Related to my point 3, to keep UFL general, I think that the element
> >>>>>>> should be passed, and not just the degree. It is conceivable that
> >>>>>>> something other than continuous Lagrange elements could be used, which
> >>>>>>> is why an element rather than a degree should be supplied.
> >>>>>>
> >>>>>> I'd prefer if we just got the current functionality in place first
> >>>>>> (without using the now banned set_foo functions) before we make any
> >>>>>> such extensions. I can have a shot at this. If we want to extend it to
> >>>>>> other types of elements, we need to have a long discussion on how to
> >>>>>> choose the element type before we proceed.
> >>>>>
> >>>>
> >>>> I don't see the relevance of this. FFC can just create Lagrange elements
> >>>> of a given degree to pass to UFL. We don't need to discuss the element
> >>>> type at this stage.
> >>>
> >>> It's harder than that since we may have both scalar and vector-valued
> >>> elements.
> >>
> >> You have to deal with construction of scalar or vector-valued elements
> >> anyway.
> >
> > Yes, but my point was that it's not enough to extract a common element
> > since there may already be scalar and vector valued elments involved.
> >
> >> It's just a matter of whether this construction is done at the
> >> ffc or ufl side. The reconstruct pattern I mentioned in another mail
> >> is one way to implement the construction at the ufl side, but that can
> >> just as well be called from ffc.
> >>
> >>> Would it be enough for now to extract the following to send to UFL:
> >>>
> >>>  common_cell
> >>>  common_family
> >>>  common_degree
> >>>
> >>> ?
> >>
> >> Extract that and then do something like
> >>     element_mapping = {}
> >>     for oldelement in elements:
> >>         newelement = oldelement.reconstruct(family=common_family,
> >> cell=common_cell, degree=common_degree)
> >>         element_mapping[oldelement] = newelement
> >>     fd = preprocess(form, element_mapping=element_mapping)
> >> from ffc, then experimentation with other element types can be done
> >> later in ffc without updating ufl.
> >
> > Looks good.
> >
>
> Who's going to start where, and when?

I can try after lunch. I have a book to finish first. :-)

--
Anders